Nucleoside analogues, such as those species lacking the 3'hydroxyl group or both the 2' and 3'hydroxyl groups, of the naturally-occurring nucleosides can act as chain terminators of the DNA into which they are incorporated. Intense effort has focused on the design and use of these compounds as inhibitors of viral replication (Van Roey et al., (1990) Ann. NY Acad. Sci., 616: 29). Although the conformation of the sugar moiety in these analogues is believed to play a critical role in modulating biological activity, including the anti-HIV 1 activity mediated by derivatives such as 3'-azido-3'-deoxythymidine (AZT) and dideoxyinosine (ddI), the main problem encountered in attempting to correlate a specific type of sugar conformation with the biological activity of nucleoside analogues is that the sugar ring is quite flexible and its conformation in solution can differ markedly from its conformation in the solid state (Jagannadh, et al., (1991) Biochem. Biophys. Res. Commun., 179: 386; Plavec et al., (1992) Biochem. Biophys. Methods, 25: 253.). Thus, any structure-function analysis based solely on solid state conformational parameters would be inaccurate unless it was previously determined that both solution and solid-state conformations were the same. Some [3.1.0]-fused 2',3'-modified cyclopropane-fused dideoxynucleosides (FIG. 1A; Wu and Chattopadhyaya, (1990) Tetrahedron Lett., 46: 2587; Okabe and Sun, (1989) Tetrahedron Lett., 30: 2203; Beard et al., (1990) Carbohyd. Res., 205: 87; Codington et al., (1962) J. Org. Chem., 27:163) appear quite rigid and their altered sugar moiety shows the same conformational preference in solution as in the solid state. However, the conformation of the furanose ring in these compounds is well outside the typical range of the Northern (N) or Southern (S) geometry conformations that are characteristic of nucleosides (Koole et al., (1991) J. Org. Chem., 56: 6884). A different type of [3.1.0] fusion, an epoxide ring between carbons 4' and 6', is found in the naturally-occurring carbocyclic nucleoside analogue neplanocin C (Kinoshita et al., (1985) Nucleosides & Nucleotides, 4: 661), which allows this compound to adopt a rigid N-geometry.
In solution there is a dynamic equilibrium between N and S type furanose conformers (Taylor et al., (1990) Antiviral Chem. Chemother., 1: 163-173). The conformations of nucleosides and their analogues can be described by the geometry of the glycosyl link (syn or anti), the rotation about the exocyclic C4'-C5' bond and the puckering of the sugar ring leading to formation of the twist and envelope conformations. Two conformations are preferred for ribose ring puckering: C3'-endo (N) and C2'-endo (S). The endo and exo refer to displacement of the atom above or below the plane of the ribose ring, respectively. The torsion angles .chi.[C2-N1-C1'-04' (pyrimidines) or C4-N9-C1'-04' (purines)] and .gamma. (C3'-C4'-C5'-05') describe, respectively, the orientations of the base and the 5'-hydroxyl group relative to the ribose ring.
In ribonucleosides and 2'-deoxyribonucleosides, two types of sugar puckering are generally energetically preferred, namely the C3'-endo (N) and the C2'-endo (S) conformations. In DNA duplexes, a 2'-endo (S) conformation of the repeating nucleoside unit confers upon the double helix a B-conformation, whereas the 3'-endo (N) conformation induces an A-conformation double helix. The A and B forms of DNA differ in the number of base pairs per turn, the amount of rotation per base pair, the vertical rise per base pair and the helical diameter. In addition, in stretches of DNA containing alternating purines and pyrimidines, a left-handed helix called Z-DNA may form.
Since DNA in solution may exist in several different conformations, the present invention provides a means of locking DNA into a specific conformation. This can be useful in elucidating the structural requirements influencing DNA-protein, DNA-DNA and DNA-RNA interactions and the development of valuable therapeutics able to specifically block these interactions.